1. Understand how the availability of microbial genome data has revolutionised microbiology to enable the management of microbial interactions with hosts and the environment.
Knowledge and Understanding
Learning

2. Understand how gene distribution and regulation contributes to pathogenesis of viruses, bacteria and
parasites.
Knowledge and Understanding
Enquiry

3. Apply bioinformatic tools and skills to analyse microbial genomes to better understand the biology of microorganisms.
Application
Problem solving

4. Communicate microbial genome research data and their significance in a concise form appropriate for the audience.
Communication

1. Written assessment (research report) 30% 1500 words
2. Exam 70% 2 hour

Assessment 1 (learning outcomes 3 & 4) is a formal report on genome data analysis, interpreting and discussing the significance of the findings.

Assessment 2 (learning outcomes 1, 2 & 4) is a closed-book two-hour end of module exam consisting of a compulsory seen question and one unseen question selected from 3 question options.

Microbiology has been revolutionised by the ease of whole genome sequencing, enabling us to better appreciate the diversity of life on earth and the interactions of microorganisms and the environment. This module will explore the methods used to analyse microbial genomes and the genes they encode. You will be introduced to state-of-the-art bioinformatics tools and their applications: you will gain hands on experience of applying these tools to analyse sequence data to understand the biology of the microorganisms. The pathogenesis of a range of bacteria, viruses and parasites will be investigated in the context of their genome and the virulence genes they encode. The importance of genome rearrangements, resulting in antigen variation, and differential gene expression in pathogenesis will be discussed. We shall study the application of whole genome typing to understand the epidemiology of pathogens, such as during infectious disease outbreaks, including the real-time sharing of whole genome sequence data for surveillance. We will critically evaluate the use of whole genome sequencing to inform antimicrobial chemotherapy, including the challenge posed by data analysis for routine application. You will learn about the application of SSU rRNA screening and metagenomics in microbiome research, biotechnology and drug discovery.

Learning sessions will comprise lectures and computer workshops 1 x 2 hr per week.

Dale et al. (2012) From genes to genomes (3rd edition) Wiley-Blackwell (ISBN 978-0-470-68385-9)
Dale & Park (2010) Molecular genetics of bacteria (5th edition) Wiley-Blackwell (ISBN 978-0-470-74184-9)
Salyers (2011) Bacterial pathogenesis: a molecular approach (3rd edition)
Microbial genomics (journal)

Lecture room with AV facilities
IT room with bioinformatic software installed (specific software may vary from year to year)

Microbiology has been revolutionised by the ease of whole genome sequencing, enabling us to better appreciate the diversity of life on earth and the interactions of microorganisms and the environment. This module will explore the methods used to analyse microbial genomes and the genes they encode. You will be introduced to state-of-the-art bioinformatics tools and their applications: you will gain hands on experience of applying these tools to analyse sequence data to understand the biology of the microorganisms. The pathogenesis of a range of bacteria, viruses and parasites will be investigated in the context of their genome and the virulence genes they encode. The importance of genome rearrangements, resulting in antigen variation, and differential gene expression in pathogenesis will be discussed. We shall study the application of whole genome typing to understand the epidemiology of pathogens, such as during infectious disease outbreaks, including the real-time sharing of whole genome sequence data for surveillance. We will critically evaluate the use of whole genome sequencing to inform antimicrobial chemotherapy, including the challenge posed by data analysis for routine application. You will learn about the application of SSU rRNA screening and metagenomics in microbiome research, biotechnology and drug discovery.